The patch is provided by SSPXR, so it is probably more proper to ask for help there. However, there is a config SSPXR-MKS-Extras.cfg. Contained within are patches for each part that reads like:
@PART[*]:HAS[@MODULE[ModuleDeployableCentrifuge]]:NEEDS[MKS]
{
DeployedMass = #$mass$
@mass *= 0.4
@MODULE[ModuleDeployableCentrifuge]
{
DeployResource = MaterialKits
DeployResourceAmount = #$../DeployedMass$
@DeployResourceAmount *= 600
%DeployedMassModifier = #$../DeployedMass$
@DeployedMassModifier *= 0.6
}
}
I believe removing these entries (ModuleDeployableHabitat and ModuleDeployableCentrifuge) should achieve the effect you want.

Terwin, I've had some heating problems myself. I think it might have something to do with the maximum core heat of all parts on a vessel. Do you by any chance have MPUs or other parts that produce heat in excess of your reactors limits? I think radiators may always try to cool the hottest part first, even if they are under a safe limit and other cooler parts are above their safe limit. Also, I do not believe NFE reactors explode on excessive heat, I think they melt down and the core is destroyed, but the part remains intact, though I have not a great deal of experience with this.

KSPNoob, the model replacement is configured in GameData\StationPartsExpansionRedux\Patches\SSPXr-StockPartReplacements.cfg. If you were to edit/delete this file to prevent it making changes to the Squad parts and created a new config for each of the SSPXR parts I think you could have both the new and old models.
AtilaElari, as far as I know stock parts go up to 2.5m. Near Future Construction has Annular Truss type parts with larger docking ports though. My own preference is to use USI construction ports to seamlessly weld.

Well, there were a few things. First of all, my working practices aren't terribly efficient and I was finding myself with less time. Secondly, having achieved a release I thought 'well, that's done, now I can proceed at a more leisurely pace'. Thirdly, I was trying to work on more detailed parts and while I thought what was coming together wasn't terrible it wasn't terribly good either. Lastly, I'd rather hoped for these parts to fill a role in career mode, but was having trouble finding a way to make that balanced, and by the time I'd have the infrastructure myself in place the scene would be too laggy regardless.

Regarding contracts, you can press Alt-F10 to open the Contract Configurator panel and see if anything is failing to load and why. For my part I had to remove the explicit reference to Gilly in StationCore.cfg. The mission to send a crew to a station also seems to be failing, but I've not looked into why that is.

I am using GPP and GPP Secondary with FAR and it works, though I've not gotten out of the original system yet. Technically compatible at least, though if it interacts poorly with new planets I cannot say.

My current career is currently based entirely around Mark IV launch vehicles (which is to say, if it takes off from the KSC, it lands at the KSC minus it's payload and fuel. Technically any space plane would do but time is more valuable than fuel so big is beautiful), I posted a picture of my first such earlier, but I've since iterated:
It's capable of lofting a significant tonnage to orbit, my most recent mission has been to take 32,000 material kits to a low orbit space station (that I might find a loophole in my self-imposed limit) with about 1000dV left over. However here is what happened when I tried for 56,000 of the same:
Which is not a complaint. This is to be expected of designing flimsy, load bearing joints even if they are aesthetically pleasing. Slowly falling apart on the runway without any explosions was just a comical means of failure. I've probably been pushing the bounds of credulity as it is.

Right now they're just parts that sit on the terrain. I've considered fixed joint anchoring and noclip foundation parts as a possible solution (not sure if it is possible to have parts that clip through the ground but not other vessels), but right now that's a little beyond my current scope to be actively worked on.